Preheat the oven to 350 ℉. Lightly grease 10 wells in a standard 12-cup muffin tin with nonstick spray or line with silicone liners. Add 1 tablespoon of water to the empty muffin cups.
In a large bowl, sift together the flour, baking powder, baking soda, 2 teaspoons of cinnamon, nutmeg, and salt. Whisk together to combine evenly.
In a separate bowl, mix together the applesauce, honey, eggs, oil, and vanilla until well combined.
Add the wet ingredients to the flour mixture. Fold the wet ingredients into the dry ingredients until just combined.
Evenly divide the batter between the prepared muffin pan, each muffin cup holds about ¼ cup of batter.
Combine the remaining teaspoon of cinnamon with the sugar in a small bowl. Sprinkle ½ teaspoon of the cinnamon sugar mixture over each muffin.
Bake for 18-20 minutes or until a toothpick inserted into the center comes out clean.
Cool the muffins on a cooling rack for 10 minutes and then remove from the muffin tin and cool completely.
Store the cooled muffins in a sealed container at room temperature for 24 hours, or in the fridge for 3-4 days.
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Notes
Flour: Feel free to use all-purpose flour or a 1:1 gluten-free all-purpose flour in place of whole wheat flour.Honey: Feel free to use maple syrup in place of the honey. Flax Eggs: In place of the eggs, mix together ⅓ cup of water with 2 tablespoons of ground flaxseed and let sit for 5 minutes. For VEGAN muffins: Use maple syrup in place of honey and flax eggs for eggs. Nutmeg: Freshly grated nutmeg is best. If using ground nutmeg, only use ⅛ teaspoon, as it can be overwhelming.